biomod2-package | Species Distribution Modeling within an Ensemble Forecasting framework |
biomod2 | Species Distribution Modeling within an Ensemble Forecasting framework |
BIOMOD_FormatingData | Initialise the datasets for usage in 'biomod2' |
BIOMOD_ModelingOptions | Configure the modeling options for each selected model |
BIOMOD_Modeling | Run a range of species distribution models |
BIOMOD_EnsembleModeling | Create and evaluate an ensemble set of models and predictions |
BIOMOD_Projection | Project the calibrated models within 'biomod2' into new space or time |
BIOMOD_EnsembleForecasting | Ensemble projections of species over space and time |
BIOMOD_ConvertOldRun | Convert objects and outputs from BIOMOD.xx into biomod2.xx objects and outputs |
BIOMOD_LoadModels | Load models built within BIOMOD_Modeling function |
BIOMOD_RangeSize | Analysis of the range size changes |
BIOMOD_RangeSize-method | Analysis of the range size changes |
BIOMOD_RangeSize-methods | Analysis of the range size changes |
evaluate | biomod2 modeling outputs evaluation |
variables_importance | Variables importance calculation |
sre | Surface Range Envelope |
Print_Default_ModelingOptions | Get default values of BIOMOD inner models' options |
level.plot | Plot 2-dimensional data for visualizing distribution of species or environment |
multiple.plot | Plot and compare prediction maps within BIOMOD |
response.plot2 | Analysis of the 2D or 3D response curves of a model within biomod2 |
ProbDensFunc | Probability Density Function |
BinaryTransformation | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold |
BinaryTransformation-method | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold |
BinaryTransformation-methods | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold |
FilteringTransformation | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold |
FilteringTransformation-method | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold |
FilteringTransformation-methods | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold |
makeFormula | Standardized formula maker |
CustomIndexMaker | Replace default package Index help file by a custom one. |
Find.Optim.Stat | Find the threshold driving to the best evaluation score |
calculate.stat | Calculate evaluation metrics based on a misclassification table |
getStatOptimValue | get the optimal score of evaluation statistical metrics |
SampleMat2 | Sample binary vector |
DF_to_ARRAY | Convert a biomod2 data.frame (or list) into array |
LIST_to_ARRAY | Convert a biomod2 data.frame (or list) into array |
randomise_data | data set shuffling tool |
full_suffling | data set shuffling tool |
RemoveProperly | remove properly BIOMOD_Modeling outputs |
RemoveProperly-method | remove properly BIOMOD_Modeling outputs |
free | BIOMOD.projection.out setter |
free-method | BIOMOD.projection.out setter |
get_built_models | BIOMOD.models.out getters |
get_built_models-method | BIOMOD.models.out getters |
get_evaluations | BIOMOD.models.out getters |
get_evaluations-method | BIOMOD.models.out getters |
get_formal_data | BIOMOD.models.out getters |
get_formal_data-method | BIOMOD.models.out getters |
get_formal_model | biomod2 models objects class and functions |
get_formal_model-method | biomod2 models objects class and functions |
get_kept_models | BIOMOD.EnsembleModeling.out getters |
get_kept_models-method | BIOMOD.EnsembleModeling.out getters |
get_needed_models | BIOMOD.EnsembleModeling.out getters |
get_needed_models-method | BIOMOD.EnsembleModeling.out getters |
get_options | BIOMOD.models.out getters |
get_options-method | BIOMOD.models.out getters |
get_predictions | BIOMOD.models.out getters |
get_predictions-method | BIOMOD.models.out getters |
get_projected_models | BIOMOD.projection.out getters |
get_projected_models-method | BIOMOD.projection.out getters |
get_scaling_model | biomod2 models objects class and functions |
get_scaling_model-method | biomod2 models objects class and functions |
get_variables_importance | BIOMOD.models.out getters |
get_variables_importance-method | BIOMOD.models.out getters |
BIOMOD.formated.data | BIOMOD_FormatingData() outputs objects class |
BIOMOD.formated.data-class | BIOMOD_FormatingData() outputs objects class |
BIOMOD.formated.data-method | BIOMOD_FormatingData() outputs objects class |
BIOMOD.formated.data.PA | BIOMOD_FormatingData() outputs objects class |
BIOMOD.formated.data.PA-class | BIOMOD_FormatingData() outputs objects class |
BIOMOD.Model.Options-class | BIOMOD_() outputs objects class |
BIOMOD.models.out-class | BIOMOD_modelling() outputs objects class |
biomod2_model | biomod2 models objects class and functions |
biomod2_model-class | biomod2 models objects class and functions |
biomod2_ensemble_model | biomod2 models objects class and functions |
biomod2_ensemble_model-class | biomod2 models objects class and functions |
BIOMOD.EnsembleModeling.out | BIOMOD_EnsembleModeling() outputs objects class |
BIOMOD.EnsembleModeling.out-class | BIOMOD_EnsembleModeling() outputs objects class |
BIOMOD.projection.out | BIOMOD_Projection() outputs objects class |
BIOMOD.projection.out-class | BIOMOD_Projection() outputs objects class |
plot-method | BIOMOD_FormatingData() outputs objects class |
plot-method | BIOMOD_Projection() outputs objects class |
show,BIOMOD.Model.Options | BIOMOD_ModelingOptions() outputs objects class |
show-method | BIOMOD_EnsembleModeling() outputs objects class |
show-method | BIOMOD_FormatingData() outputs objects class |
show-method | BIOMOD_modelling() outputs objects class |
show-method | BIOMOD_Projection() outputs objects class |
ANN_biomod2_model | biomod2 models objects class and functions |
ANN_biomod2_model-class | biomod2 models objects class and functions |
CTA_biomod2_model | biomod2 models objects class and functions |
CTA_biomod2_model-class | biomod2 models objects class and functions |
FDA_biomod2_model | biomod2 models objects class and functions |
FDA_biomod2_model-class | biomod2 models objects class and functions |
GAM_biomod2_model | biomod2 models objects class and functions |
GAM_biomod2_model-class | biomod2 models objects class and functions |
GBM_biomod2_model | biomod2 models objects class and functions |
GBM_biomod2_model-class | biomod2 models objects class and functions |
GLM_biomod2_model | biomod2 models objects class and functions |
GLM_biomod2_model-class | biomod2 models objects class and functions |
MARS_biomod2_model | biomod2 models objects class and functions |
MARS_biomod2_model-class | biomod2 models objects class and functions |
MAXENT_biomod2_model | biomod2 models objects class and functions |
MAXENT_biomod2_model-class | biomod2 models objects class and functions |
RF_biomod2_model | biomod2 models objects class and functions |
RF_biomod2_model-class | biomod2 models objects class and functions |
SRE_biomod2_model | biomod2 models objects class and functions |
SRE_biomod2_model-class | biomod2 models objects class and functions |
EMca_biomod2_model | biomod2 models objects class and functions |
EMca_biomod2_model-class | biomod2 models objects class and functions |
EMci_biomod2_model | biomod2 models objects class and functions |
EMci_biomod2_model-class | biomod2 models objects class and functions |
EMcv_biomod2_model | biomod2 models objects class and functions |
EMcv_biomod2_model-class | biomod2 models objects class and functions |
EMmean_biomod2_model | biomod2 models objects class and functions |
EMmean_biomod2_model-class | biomod2 models objects class and functions |
EMmedian_biomod2_model | biomod2 models objects class and functions |
EMmedian_biomod2_model-class | biomod2 models objects class and functions |
EMwmean_biomod2_model | biomod2 models objects class and functions |
EMwmean_biomod2_model-class | biomod2 models objects class and functions |
predict-method | biomod2 models objects class and functions |
show-method | biomod2 models objects class and functions |
get_var_range | biomod2 models objects class and functions |
get_var_type | biomod2 models objects class and functions |
BIOMOD.stored.array | BIOMOD.stored.xxx objects class |
BIOMOD.stored.array-class | BIOMOD.stored.xxx objects class |
BIOMOD.stored.data.frame | BIOMOD.stored.xxx objects class |
BIOMOD.stored.data.frame-class | BIOMOD.stored.xxx objects class |
BIOMOD.stored.data | BIOMOD.stored.xxx objects class |
BIOMOD.stored.data-class | BIOMOD.stored.xxx objects class |
BIOMOD.stored.files | BIOMOD.stored.xxx objects class |
BIOMOD.stored.files-class | BIOMOD.stored.xxx objects class |
BIOMOD.stored.formated.data | BIOMOD.stored.xxx objects class |
BIOMOD.stored.formated.data-class | BIOMOD.stored.xxx objects class |
BIOMOD.stored.models.options | BIOMOD.stored.xxx objects class |
BIOMOD.stored.models.options-class | BIOMOD.stored.xxx objects class |
BIOMOD.stored.models.out | BIOMOD.stored.xxx objects class |
BIOMOD.stored.models.out-class | BIOMOD.stored.xxx objects class |
BIOMOD.stored.raster.stack | BIOMOD.stored.xxx objects class |
BIOMOD.stored.raster.stack-class | BIOMOD.stored.xxx objects class |
load_stored_object | BIOMOD.stored.objects functions |
load_stored_object-method | BIOMOD.stored.objects functions |
disk.pseudo.abs.selection | biomod2 internal functions |
disk.pseudo.abs.selection-method | biomod2 internal functions |
random.pseudo.abs.selection | biomod2 internal functions |
random.pseudo.abs.selection-method | biomod2 internal functions |
sre.pseudo.abs.selection | biomod2 internal functions |
sre.pseudo.abs.selection-method | biomod2 internal functions |
user.defined.pseudo.abs.selection | biomod2 internal functions |
user.defined.pseudo.abs.selection-method | biomod2 internal functions |
Projection | biomod2 internal functions |
Projection-method | biomod2 internal functions |
.Models.prepare.data | biomod2 internal functions |
.Models.prepare.data-method | biomod2 internal functions |
.Projection.do.proj | biomod2 internal functions |
.Projection.do.proj-method | biomod2 internal functions |
.transform.outputs | biomod2 internal functions |
.transform.outputs-method | biomod2 internal functions |
check_data_range | biomod2 models objects class and functions |
response.plot | Analysis of the response curves of a model within Biomod |
getEMalgos | biomod2 deprecated functions |
getEMalgos-method | biomod2 deprecated functions |
getEMbuiltModels | biomod2 deprecated functions |
getEMbuiltModels-method | biomod2 deprecated functions |
getEMeval | biomod2 deprecated functions |
getEMeval-method | biomod2 deprecated functions |
getEMkeptModels | biomod2 deprecated functions |
getEMkeptModels-method | biomod2 deprecated functions |
getEM_needed_models | biomod2 deprecated functions |
getEM_needed_models-method | biomod2 deprecated functions |
getFormalModel | biomod2 deprecated functions |
getFormalModel-method | biomod2 deprecated functions |
getModelsBuiltModels | biomod2 deprecated functions |
getModelsBuiltModels-method | biomod2 deprecated functions |
getModelsEvaluations | biomod2 deprecated functions |
getModelsEvaluations-method | biomod2 deprecated functions |
getModelsInputData | biomod2 deprecated functions |
getModelsInputData-method | biomod2 deprecated functions |
getModelsOptions | biomod2 deprecated functions |
getModelsOptions-method | biomod2 deprecated functions |
getModelsPrediction | biomod2 deprecated functions |
getModelsPrediction-method | biomod2 deprecated functions |
getModelsPredictionEval | biomod2 deprecated functions |
getModelsPredictionEval-method | biomod2 deprecated functions |
getModelsVarImport | biomod2 deprecated functions |
getModelsVarImport-method | biomod2 deprecated functions |
getProjection | biomod2 deprecated functions |
getProjection-method | biomod2 deprecated functions |
getScalingModel | biomod2 deprecated functions |
getScalingModel-method | biomod2 deprecated functions |